Biology subjects

Solomon, A.

Publications and source records attributed to Solomon, A..

13 recordsLinked to original sources

bioRxiv2025

Dynamics of Macrophage Polarization Reveal Unique Phenotypes During Mouse Postpartum Uterine Remodeling

BackgroundMacrophages play essential roles in uterine physiology during pregnancy and the postpartum (PP) period. In various organ systems, macrophages exhibit distinct M1 (pro-inflammatory) and M2 (anti-inflammatory) polarization states, the balance of which is key not only in scarless wound healing but also in pathological fibrosis. While macrophages are central players in PP uterine remodeling, their polarization dynamics during this period and associated spatial distribution remain largely unknown. MethodsUterine tissues were collected from C57BL/6J wild-type mice at various PP days (PPD 1, 3, 7, 14, 21, 28) and non-pregnant controls. Multicolor flow cytometry was used to analyze immune populations and macrophage polarization states. Macrophage polarization was determined using CD86 (M1 marker) and CD206 (M2 marker). Immunofluorescence (IF) and immunohistochemistry (IHC) were used to examine the colocalization of M1 and/or M2 markers alongside F4/80 to assess macrophage polarization status and tissue distribution. ResultsOn PPD1, uterine macrophage numbers were higher compared to all other time points, with significantly increased M2 macrophages (CD86-CD206+) (43% p<0.0001) compared to PPD3 (5.1%), PPD7 (2.4%), PPD14 (2.3%), and non-pregnant (1.9%). A rapid polarization shift to M1 macrophages (CD86+CD206-) occurred on PPD3 (50.6%), PPD7 (66.5%), and PPD14 (58.8%) compared to PPD1 (11.9% p<0.0001). Additionally, there was a trend of increased M2 macrophages on PPD21 (10%) and PPD28 (5%). We observed a unique macrophage subset of mixed phenotype (co-expressing CD86+CD206+) significantly higher on PPD 1 (37.2% p<0.05) compared to NP (7.8%), PPD7 (11.6%), and PPD14 (26.4%). IF co-staining confirmed these dynamics, showing the highest percentage of macrophages co-expressing CD206+F4/80+ on PPD1 (77.2%), significantly higher than all other time points. IHC revealed the specific temporal and spatial distribution of F4/80+ and CD206+ cells within the uterine endometrial stroma adjacent to the myometrial junction in the early PP period. ConclusionsThe predominance of M2-polarized macrophages on PPD1 followed by a rapid shift to M1 phenotype from PPD3 to PPD14 indicates an evolving inflammatory response during the early postpartum period. Repolarization to M2 profile on PPD21, along with increased abundance of a mixed population (M1/M2), uncovers the dynamic complexity of macrophage polarization during PP uterine remodeling, providing new insights into scarless uterine tissue repair.

immunology↗

bioRxiv2024

Analysis of a hypomorphic mei-P26 mutation reveals developmental control of CO patterning mechanisms

Female gametogenesis in Drosophila requires differentiation and mitotic division of germ cells, acquisition of oocyte fate, and entry into meiosis. Each of these processes is well understood individually; however, little is known about the mechanisms that ensure proper temporal integration of germ cell differentiation and meiotic chromosome dynamics. Here, we take advantage of a hypomorphic mutation in mei-P26, a well-characterized gene with multiple diverse functions in germ cell development, to determine the consequences of disrupting the coordination between development and meiosis. While null mutations in mei-P26 lead to tumorous ovaries, the hypomorphic allele mei-P261 allows sufficient germ cell differentiation and fertility to support analysis of meiotic chromosome dynamics. Unlike wildtype germaria, 60% of cysts in mei-P261 germaria co-express the differentiation factor Bag of marbles (Bam) and the oocyte specification factor Orb, suggesting that mitotic division is delayed. In this context, the synaptonemal complex rarely assembles into full length continuous tracks and instead is missing or present only as foci. Despite these phenotypes, meiotic double-strand breaks still form and are repaired as crossovers, but the crossovers are mis-patterned and form in centromere proximal regions rather than chromosome arms. The strength of crossover interference is significantly reduced and the centromere effect is lost, but crossover assurance is intact and the meiosis-specific machinery is used to form crossovers. We suggest a model where the failure to exit mitosis in a timely fashion causes cells to enter meiosis while still receiving mitotic signals, resulting in abnormal meiotic chromosome dynamics and impaired crossover formation. Article summaryFemale gametogenesis in Drosophila requires the precise temporal integration of germ cell differentiation and meiotic entry. Using a hypomorphic mutation in mei-P26, we investigated how disrupting this coordination affects meiotic chromosome dynamics. In mei-P261 mutants, delayed mitotic exit causes cells to enter meiosis while still receiving mitotic signals. This results in fragmented synaptonemal complex and the loss of some but not all CO patterning mechanisms. These results suggest that timely mitotic exit is critical for establishing the proper regulatory landscape required for meiotic recombination.

genetics↗

bioRxiv2024

Mouse PAW: reverse-translating the FINGER multimodal lifestyle intervention enhances synaptic plasticity and cognition in adult wild type female mice

BackgroundTargeting multiple risk factors through preventive interventions can halt the onset or progression of dementia. The clinical efficacy of this approach was shown in the multimodal FINGER trial, yet knowledge of the underlying biological mechanisms is limited. In the current study, we applied for the first time a multimodal lifestyle intervention in mice to study effects on cognition and associated molecular pathways. MethodsWe have established a novel experimental model, the lifestyle intervention PAW (Prevention of Alzheimers by a Multimodal Lifestyle Protocol - Working-mechanisms for Memory Gains) in mice. In this model, we combined different modalities of intervention aiming to achieve synergistic effects. The animals were given access to running wheels (voluntary exercise), Fortasyn Connect (a medical food that slows disease progression in early Alzheimers disease), and they were subjected to cognitive training in an IntelliCage environment (PAW group). To separately investigate the effects of pharmacological vascular management as a preventive measure, another group of mice was given Atorvastatin and Enalapril (cholesterol and blood pressure lowering pharmaceuticals, respectively) dosed in the diet (Pharma group). Control mice were housed in normal conditions. We included 12 wild type C57BL/6J female mice 6.5 months of age per group. The full intervention lasted for 8 weeks. Blood pressure was measured at baseline and the end of the intervention. All mice underwent a battery of behavioural testing after the eight weeks of intervention. Hippocampi were dissected for proteomics analysis. ResultsDuring the intervention, the PAW group actively participated in the intervention by learning the different cognitive training programs and by using the running wheels. At the end of the intervention, the PAW group showed a lowering of blood pressure to a similar extent as in the Pharma group (systolic 158 mmHg to 139 mmHg, p = 0.003, and 163 mmHg to 136 mmHg, p = 0.042, respectively). Furthermore, the PAW group displayed a better short-term spatial working memory compared to the control group as assessed by the spontaneous alternation in the Y maze test (66.5% and 56.7%, respectively, p = 0.036). Proteomic analysis of the hippocampi and downstream bioinformatic analysis revealed that several pathways were upregulated in the PAW mice including synaptogenesis (Z = 4.27, p = 1.26E-18) and glutamate binding, activation of AMPA receptors and synaptic plasticity (Z = 3.74, p = 3.16E-19). ConclusionsOur findings suggest that the PAW model effectively mimics the clinical effects of multimodal lifestyle dementia prevention, and further demonstrates the activation of hippocampal-specific molecular drivers of memory gains.

neuroscience↗

bioRxiv2024

Early and Delayed STAT1-Dependent Responses Drive Local Trained Immunity of Macrophages in the Spleen

Trained immunity (TI) is the process wherein innate immune cells gain functional memory upon exposure to specific ligands or pathogens, leading to augmented inflammatory responses and pathogen clearance upon secondary exposure. While the differentiation of hematopoietic stem cells (HSCs) and reprogramming of bone marrow (BM) progenitors are well-established mechanisms underpinning durable TI protection, remodeling of the cellular architecture within the tissue during TI remains underexplored. Here, we study the effects of peritoneal Bacillus Calmette-Guerin (BCG) administration to find TI-mediated protection in the spleen against a subsequent heterologous infection by the Gram-negative pathogen Salmonella Typhimurium (S.Tm). Utilizing single cell RNA-sequencing and flow cytometry, we discerned STAT1-regulated genes in TI-associated resident and recruited splenic myeloid populations. The temporal dynamics of TI were further elucidated, revealing both early and delayed myeloid subsets with time-dependent, cell type-specific STAT1 signatures. Using lineage tracing, we find that tissue-resident red pulp macrophages (RPM), initially depleted by BCG exposure, are restored from both tissue-trained, self-renewing macrophages and from bone marrow-derived progenitors, fostering long lasting local defense. Early inhibition of STAT1 activation, using specific JAK-STAT inhibitors, reduces both RPM loss and recruitment of trained monocytes. Our study suggests a temporal window soon after BCG vaccination, in which STAT1-dependent activation of long-lived resident cells in the tissue mediates localized protection.

immunology↗

bioRxiv2023

Monocyte-derived microglia with Dnmt3a mutation cause motor pathology in aging mice

Microglia are established in embryogenesis forming a self-containing cellular compartment resisting seeding with cells derived from adult definitive hematopoiesis. We report that monocyte-derived macrophages (MoM{Phi}) accumulate in the brain of aging mice with distinct topology, including the nigrostriatum and medulla, but not the frontal cortex. Parenchymal MoM{Phi} adopt bona fide microglia expression profiles. Unlike microglia, these monocyte-derived microglia (MoMg) are due to their hematopoietic origin targets of clonal hematopoiesis (CH). Using a chimeric transfer model, we show that hematopoietic expression of DNMT3AR822H, a prominent mutation in human CH, renders MoMg pathogenic promoting motor deficits resembling atypical Parkinsonian disorders. Collectively, these data establish in a mouse model that MoMg progressively seed the brains of aging healthy mice, accumulate in selected areas, and, when carrying a somatic mutation associated with CH, can contribute to brain pathology.

immunology↗

bioRxiv2023

Machine learning prediction of future amyloid beta positivity in amyloid-negative individuals

INTRODUCTIONThe pathophysiology of Alzheimers disease (AD) involves {beta}-amyloid (A{beta}) accumulation. Early identification of individuals with abnormal {beta}-amyloid levels is crucial, but A{beta} quantification with positron emission tomography (PET) and cerebrospinal fluid (CSF) is invasive and expensive. METHODSWe propose a machine learning framework using standard non-invasive (MRI, demographics, APOE, neuropsychology) measures to predict future A{beta}-positivity in A{beta}-negative individuals. We separately study A{beta}-positivity defined by PET and CSF. RESULTS: Cross-validated AUC for 4-year A{beta} conversion prediction was 0.78 for the CSF-based and 0.68 for the PET-based A{beta} definitions. Although not trained for the clinical status-change prediction, the CSF-based model excelled in predicting future mild cognitive impairment (MCI)/dementia conversion in cognitively normal/MCI individuals (AUCs, respectively, 0.76 and 0.89 with a separate dataset). DISCUSSIONStandard measures have potential in detecting future A{beta}-positivity and assessing conversion risk, even in cognitively normal individuals. The CSF-based definition led to better predictions than the PET-based definition.

neuroscience↗

bioRxiv2022

Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks

Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA-sequencing (scRNA-seq) are increasingly used to study the host factors underlying diverse cellular phenotypes. But current approaches do not permit the simultaneous unbiased study of both host and bacterial factors during infection. Here, we developed scPAIR-seq, an approach to analyze both host and pathogen factors during infection by combining multiplex-tagged mutant bacterial library with scRNA-seq to identify mutant-specific changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We developed a pipeline to independently analyze redundancy between effectors and mutant-specific unique fingerprints, and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.

microbiology↗

bioRxiv2022

Inflammatory signals from fatty bone marrow supports the early stages of DNMT3a driven clonal hematopoiesis

Age related cancer is not only due to the random accumulation of mutations, but also how phenotypes are selected by the aging environment. While fatty bone marrow (FBM), is one of the hallmarks of bone marrow ageing, it is unknown whether FBM can modify the evolution of the early stages of leukemia and clonal hematopoiesis (CH). To address this question, we established FBM mice models and transplanted both human and mice preleukemic hematopoietic stem cells (PreL-HSCs) carrying DNMT3A mutations. We demonstrate that castration which models age related andropenia result in FBM. A significant increase in self-renewal was found when DNMT3AMut - preL-HSPCs were exposed to FBM. To better understand the mechanisms of the FBM-preL-HSPCs interaction, we performed single cell RNA-sequencing on HSPCs three days after FBM exposure. A 20-50 fold increase in DNMT3AMut-preL-HSCs was observed under FBM conditions in comparison to other conditions. PreL-HSPCs exposed to FBM exhibited an activated inflammatory signaling (IL-6 and INF{gamma}). Cytokine analysis of BM fluid demonstrated increased IL-6 levels under FBM conditions. Anti-IL-6 neutralizing antibodies significantly reduced the selective advantage of DNMT3AMut-preL-HSPCs exposed to FBM. Overall, age related paracrine FBM inflammatory signals promote DNMT3A-driven clonal hematopoiesis, which can be inhibited by blocking the IL-6 receptor.

cancer biology↗

bioRxiv2021

Uncovering the modified immunopeptidome reveals insights into principles of PTM-driven antigenicity

Antigen processing and presentation are critical for modulating tumor-host interactions. While post-translational modifications (PTMs) can alter the binding and recognition of antigens, their identification remains challenging. Here we uncover the role PTMs may play in antigen presentation and recognition in human cancers by profiling 29 different PTM combinations in immunopeptidomics data from multiple clinical samples and cell lines. We established and validated an antigen discovery pipeline and showed that newly identified modified antigens from a murine cancer model are cancer-specific and can elicit T cell killing. Systematic analysis of PTMs across multiple cohorts defined new haplotype preferences and binding motifs in association with specific PTM types. By expanding the antigenic landscape with modifications, we uncover disease-specific targets, including thousands of novel cancer-specific antigens and reveal insight into PTM-driven antigenicity. Collectively, our findings highlight an immunomodulatory role for modified peptides presented on HLA I, which may have broad implications for T-cell mediated therapies in cancer and beyond. SignificanceMajor efforts are underway to identify cancer-specific antigens for personalized immunotherapy. Here, we enrich the immunopeptidome landscape by uncovering thousands of novel putative antigens that are post-translationally modified. We define unique preferences for PTM-driven alterations affecting HLA binding and TCR recognition, which in turn alter tumor-immune interactions. Conflict of interest statementAuthors declare no conflicts of interest.

cancer biology↗

bioRxiv2021

scRNA-seq Reveals A Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella

Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population defined by unique molecular features, but the implications to their function during infection is unknown. Here, we applied high resolution kinetic analysis using microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe an eclipse like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue resident red pulp macrophages. A second phase involved bacterial growth mediated by intracellular replication within a macrophage population we termed CD9 macrophages, that originate from non-classical monocytes. Nr4a1e2-/- mice, specifically depleted of non-classical monocytes but not other mononuclear cells, are more resistant to S.Tm infection. Our study underscores a cell-type specific host-pathogen interaction that determines early infection growth dynamics and has implications to the infection outcome of the entire organism.

immunology↗

bioRxiv2017

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.

Understanding the molecular programs that guide cellular differentiation during development is a major goal of modern biology. Here, we introduce an approach, WADDINGTON-OT, based on the mathematics of optimal transport, for inferring developmental landscapes, probabilistic cellular fates and dynamic trajectories from large-scale single-cell RNA-seq (scRNA-seq) data collected along a time course. We demonstrate the power of WADDINGTON-OT by applying the approach to study 65,781 scRNA-seq profiles collected at 10 time points over 16 days during reprogramming of fibroblasts to iPSCs. We construct a high-resolution map of reprogramming that rediscovers known features; uncovers new alternative cell fates including neuraland placental-like cells; predicts the origin and fate of any cell class; highlights senescent-like cells that may support reprogramming through paracrine signaling; and implicates regulatory models in particular trajectories. Of these findings, we highlight Obox6, which we experimentally show enhances reprogramming efficiency. Our approach provides a general framework for investigating cellular differentiation.

bioinformatics↗

bioRxiv2017

Age-specific prevalence of anti-Pgp3 antibodies and severe conjunctival scarring in the Solomon Islands

BackgroundTrachomatous trichiasis (TT) and ocular Chlamydia trachomatis (Ct) infection in the Solomon Islands are scarce, whereas trachomatous inflammation-follicular (TF) is prevalent.\n\nMethodsWe enrolled 1511 people aged [≥]1 year from randomly selected households in 13 villages in which >10% of the population had TF prior to a single round of azithromycin MDA undertaken six months previously. Blood was collected from people of all ages to be screened for anti-Pgp3 antibodies. Photographs were collected from people of all ages for analysis of scarring severity.\n\nResultsConjunctival scars were visible in 13.1% of photographs. Mild (p<0.0001) but not severe (p=0.149) scars increased in prevalence with age. Anti-Pgp3 antibody seroprevalence was 18% in 1-9 year olds, increased sharply around the age of sexual debut, and reached 69% in those over 25 years. Anti-Pgp3 seropositivity did not increase significantly between the ages of 1-9 years, and was not associated with scarring in children (p=0.472) or TF in children (p=0.581).\n\nConclusionsSigns of trachoma are common in the Solomon Islands but occur frequently in individuals who have no serological evidence of prior ocular infection with Ct. WHO recommendations for directing MDA provision based on signs alone may not be suitable in this context.

epidemiology↗

bioRxiv2017

Active Trachoma Cases In The Solomon Islands Have Varied Polymicrobial Community Structures But Do Not Associate With Individual Non-Chlamydial Pathogens Of The Eye

BackgroundSeveral non-chlamydial microbial pathogens are associated with clinical signs of active trachoma in trachoma-endemic communities with a low prevalence of ocular Chlamydia trachomatis (Ct) infection. In the Solomon Islands, the prevalence of Ct among children is low despite the prevalence of active trachoma being moderate. We therefore set out to investigate whether active trachoma was associated with a common non-chlamydial infection or with a dominant polymicrobial community dysbiosis in the Solomon Islands.\n\nMethodsWe studied DNA from conjunctival swabs collected from 257 Solomon Islanders with active trachoma and matched controls. Droplet digital PCR was used to test for pathogens suspected to be able to induce follicular conjunctivitis. Polymicrobial community diversity and composition were studied by sequencing of hypervariable regions of the 16S ribosomal ribonucleic acid gene in a subset of 54 cases and 53 controls.\n\nResultsAlthough Ct was associated with active trachoma, the number of infections was low (cases: 3.9%, controls: 0.4%). Estimated prevalence (cases, controls) of each non-chlamydial infection was as follows: S. aureus (1.9%, 1.9%), Adenoviridae (1.2%, 1.2%), coagulase-negative Staphylococcus (5.8%, 4.3%), H. influenzae (7.4%, 11.7%), M. catarrhalis (2.3%, 4.7%) and S. pneumoniae (7.0%, 6.2%). There was no statistically significant association between clinical signs of trachoma and presence or load of any of the non-Ct infections that were assayed. Inter-individual variations in the conjunctival microbiome were characterised by differences in the levels of Corynebacterium, Proprionibacterium, Helicobacter and Paracoccus, but diversity and relative abundance of these specific genera did not differ significantly between cases and controls.\n\nDiscussionIt is unlikely that the prevalent trachoma-like follicular conjunctivitis in the Solomon Islands has a dominant bacterial aetiology. Before implementing community-wide azithromycin distribution for trachoma, policy makers should consider that clinical signs of trachoma can be observed in the absence of any detectable azithromycin-susceptible organism.

microbiology↗